Contacts of the strand formed by residues 398 - 403 (chain E) in PDB entry 4ZXB
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with TYR 398 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367E TYR* 3.6 4.5 - - - +
393E LEU* 3.5 6.0 - - - +
394E GLU* 2.8 34.2 + - + +
395E ILE 3.4 24.2 - - - -
396E GLY* 3.6 16.5 + - - -
397E ASN* 1.3 76.3 - - - +
399E SER* 1.3 59.9 + - - +
400E PHE 4.3 6.5 - - - +
401E TYR* 3.8 28.0 - + + +
425E LYS* 3.3 28.2 + - + +
426E LEU 3.6 25.4 - - - -
427E PHE* 3.7 30.7 - + + -
455E ASN 5.3 0.3 + - - -
456E ASP* 2.7 29.6 + - - -
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Residues in contact with SER 399 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367E TYR* 3.3 12.6 - - - -
368E LEU 2.9 23.4 + - - -
388E ILE* 3.7 9.7 - - - +
390E GLY* 4.1 9.6 - - - -
393E LEU* 3.6 13.2 - - - +
398E TYR* 1.3 73.0 - - - +
400E PHE* 1.3 62.2 + - - +
401E TYR* 5.6 0.4 - - - -
421E ILE* 3.1 20.0 - - - +
423E GLN 2.9 28.9 + - - -
424E GLY 3.3 9.7 - - - -
425E LYS 2.9 5.2 + - - +
426E LEU* 5.2 0.3 - - - +
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Residues in contact with PHE 400 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368E LEU* 3.3 40.6 - - + -
370E ILE* 3.7 11.7 - - + -
379E LEU* 3.7 25.6 - - + -
388E ILE* 4.2 7.4 - - + -
398E TYR* 4.3 0.7 - - - +
399E SER* 1.3 80.0 + - - +
401E TYR* 1.3 62.0 + - - +
402E ALA* 4.0 12.6 - - + -
411E LEU* 4.2 5.4 - - + -
412E TRP* 4.2 5.2 - + - -
421E ILE* 4.4 7.2 - - + -
425E LYS 3.4 4.2 + - - +
426E LEU* 3.3 21.5 - - + -
427E PHE* 3.0 23.0 + - - +
428E PHE* 3.5 39.3 - + - -
442E MET* 3.6 24.5 - - + -
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Residues in contact with TYR 401 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367E TYR* 5.8 1.1 - - + -
368E LEU 3.0 8.6 + - - +
369E LYS* 3.2 38.5 + - + -
370E ILE* 2.7 29.1 + - - +
394E GLU* 3.8 29.2 - - + -
395E ILE* 4.8 2.9 - - + -
398E TYR* 3.8 18.4 - + + +
399E SER 5.6 0.2 - - - -
400E PHE* 1.3 77.6 - - - +
402E ALA* 1.3 60.3 + - - +
403E LEU* 3.6 29.6 - - + +
427E PHE* 3.5 57.7 - + + -
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Residues in contact with ALA 402 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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370E ILE* 3.2 9.6 - - + +
400E PHE* 4.0 9.6 - - + -
401E TYR* 1.3 74.2 - - - +
403E LEU* 1.3 60.4 + - - +
405E ASN* 3.9 9.0 - - - +
408E LEU* 5.1 6.5 - - + -
427E PHE* 2.8 10.9 + - - +
428E PHE* 3.3 32.2 - - + -
429E HIS 3.1 24.6 + - - -
431E ASN* 3.1 11.5 + - - +
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Residues in contact with LEU 403 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369E LYS* 5.8 0.4 - - - -
370E ILE 2.9 9.8 + - - +
371E ARG* 3.2 20.8 - - + +
372E ARG* 3.0 19.6 + - + -
401E TYR* 3.6 37.2 - - + +
402E ALA* 1.3 75.2 - - - +
404E ASP* 1.3 74.3 + - + +
405E ASN* 3.5 3.9 + - - -
427E PHE* 4.0 6.5 - - + -
429E HIS* 3.2 20.4 - - + +
430E TYR* 3.9 19.7 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il